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An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection

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An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by T-Stór An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection Kerstin Diekmann1,2, Trevor R. Hodkinson2, Evelyn Fricke1, Susanne Barth1* 1 Teagasc Crops Research Centre, Carlow, Ireland, 2 Department of Botany, School of Natural Sciences, Trinity College Dublin, University of Dublin, Dublin, Ireland Abstract Background: Obtaining chloroplast genome sequences is important to increase the knowledge about the fundamental biology of plastids, to understand evolutionary and ecological processes in the evolution of plants, to develop biotechnological applications (e.g. plastid engineering) and to improve the efficiency of breeding schemes. Extraction of pure chloroplast DNA is required for efficient sequencing of chloroplast genomes. Unfortunately, most protocols for extracting chloroplast DNA were developed for eudicots and do not produce sufficiently pure yields for a shotgun sequencing approach of whole plastid genomes from the monocot grasses. Methodology/Principal Findings: We have developed a simple and inexpensive method to obtain chloroplast DNA from grass species by modifying and extending protocols optimized for the use in eudicots. Many protocols for extracting chloroplast DNA require an ultracentrifugation step to efficiently separate chloroplast DNA from nuclear DNA. The developed method uses two more centrifugation steps than previously reported protocols and does not require an ultracentrifuge. Conclusions/Significance: The described method delivered chloroplast DNA of very high quality from two grass species belonging to highly different taxonomic subfamilies within the grass family (Lolium perenne, Pooideae; Miscanthus6gi- ganteus, Panicoideae). The DNA from Lolium perenne was used for whole chloroplast genome sequencing and detection of SNPs. The sequence is publicly available on EMBL/GenBank. Citation: Diekmann K, Hodkinson TR, Fricke E, Barth S (2008) An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection. PLoS ONE 3(7): e2813. doi:10.1371/journal.pone.0002813 Editor: Ivan Baxter, Purdue University, United States of America Received May 1, 2008; Accepted July 3, 2008; Published July 30, 2008 Copyright: ß 2008 Diekmann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: KD was financed under the Teagasc Walsh Fellowship Schema. Project funding was obtained from the Teagasc ‘Vision’ programme. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction other economic crops [6]. Plastid genome sequences from this family are of high importance and are needed for a whole range of Chloroplasts are a form of plastid, derived originally from applications. independent living cyanobacteria that were incorporated into plant Plastid genome sequences offer new engineering targets for cells during evolution [1,2,3]. Up to 300 chloroplasts [4] can be biotechnology as transgenes are normally integrated into interge- found in one plant cell where they are the location of photosynthesis. nic spacer regions. Therefore it is necessary to know the exact In most species chloroplasts are usually strictly maternally inherited chloroplast genome sequence of the target species to design [5]. Due to their endosymbiotic origins chloroplasts contain their species-specific vectors to ensure the engineering success [7]. So own genome that generally shows highly conserved features far, for example, genes for insect [8], herbicide [9] or disease regarding gene content and gene order between species. Thus, resistance [10] have been integrated into the tobacco chloroplast chloroplast genome sequences are important to improve knowledge genome and might also be useful for integration into the about the fundamental biology of plastids, to help understand chloroplast genome of Poaceae species. To date, plastid engineer- evolutionary and ecological processes in plants, to facilitate the ing has been successfully optimized for only one monocot species, development of biotechnological applications (e.g. plastid engineer- Oryza sativa, of the grass family (Poaceae) [11,12]. Furthermore ing), and to improve the efficiency of breeding schemes. detailed characterization of plastid haplotypes is essential for To date, more than 100 complete chloroplast genome sequences thorough studies of the population genetic, phylogenetic and of land plant species are publicly available (http://www.ncbi.nlm. taxonomic background of grass species [13]. Chloroplast DNA nih.gov/genomes/ORGANELLES /plastids_tax.html) and most (cpDNA) sequences are also important for conventional plant are from angiosperms, especially eudicots (60 sequences) and breeding programmes to characterize and hence manipulate monocots (17 sequences). Many agricultural plant species belong organelle genomes by breeding. Besides, they are of interest to to either of these two groups but the monocot grass family Poaceae is investigate nucleo-cytoplasmic effects [14] since plastid signals by far the most important globally from a socio-economic controlling nuclear gene expression can have both positive and perspective as it contains the cereals, forage species and several negative effects on gene expression [15]. PLoS ONE | www.plosone.org 1 July 2008 | Volume 3 | Issue 7 | e2813 Grass CpDNA Isolation Protocol Complete cpDNA sequences are in general obtained by Results and Discussion sequencing either cpDNA clones found as ‘contaminations’ in genomic libraries [e.g. 16] or by sequencing high purity extracted Improved isolation methods for cpDNA from grass species are cpDNA that has been cloned into sequencing vectors [e.g. 17]. of high socio-economic value for a range of applications in this Recently a primer walking strategy, based on consensus cpDNA highly valuable family (Poaceae). In this study we have optimized a sequencing primers (CCSPs) designed from the chloroplast procedure to extract very pure Miscanthus cpDNA of high quantity genome of Nicotiana tabacum in comparison with the chloroplast (70 mg/100 g starting leaf material) and very pure Lolium cpDNA genome of Arabidopsis thaliana and Spinacia oleracea, was used for of lower quantity (0.3 mg/100 g starting material). For both obtaining complete chloroplast genome sequences [18]. We were species the successful isolation of the chloroplast genome was especially interested in the chloroplast genome of perennial determined by restriction digestion of the DNA visualized by ryegrass (Lolium perenne L.) which is also a member of Poaceae agarose gel electrophoresis. The fine banding patterns were, in and one of the most important forage crops in Europe. both cases, similar to the fine cpDNA banding patterns from other We aimed to sequence the complete cpDNA genome of L. perenne species typical for digested cpDNA (Fig. 1). The latter Lolium and therefore chose to extract pure cpDNA from a perennial extract was subject to whole genome amplification using the ryegrass population and to sequence it using a shotgun sequencing GenomePhi DNA amplification kit (Amersham Biosciences, Prod.- approach. We used this approach because it is cost and time effective no.: 25-6600-01) following the manufacturer’s instructions. The and it allowed us to assess nucleotide variation within the chloroplast sequencing of the entire cpDNA of Lolium using a classical shotgun genome of a cross pollinating grass species by documenting the sequencing approach and its pre-assembly was carried out by a occurrence of single nucleotide polymorphisms (SNPs). SNPs are company (GATC Biotech AG, Konstanz, Germany). The result useful to detect chloroplast haplotype variation in individual plants of confirmed, once more, our presumption that the isolated DNA a cultivar and to help identify cytoplasmic gene pools. They can be was Lolium cpDNA and it enabled us to assemble the entire used to evaluate the mutation rate in chloroplast genomes and to chloroplast genome of L. perenne. The sequence in complete length detect sequences belonging to mitochondrial or nuclear DNA with a produced with this method is available on EMBL, GenBank or high similarity to the chloroplast genome (e.g. greater than 98 %) DDBJ (Accession number: AM777385). [19]. Therefore SNPs might also help to obtain information about horizontal gene transfer within a species. Although general protocols for DNA extraction from plants are well developed [see 20 for a review], the success of cpDNA extractions is highly species dependent [21]. Most of the available protocols for cpDNA extraction were designed and established using eudicot plants such as the protocol developed by 22 for pea (Pisum). We tried several of these protocols [e.g. 21, 22, 23] but found that they were unreliable for application in grasses. Possibly because of the high fibre content of grass leaves, cpDNA yields obtained with these methods were not high or pure enough (Figure S1) for whole chloroplast genome sequencing using the shotgun sequencing approach. Therefore we combined and modified existing protocols to develop a simple, robust and inexpensive method for isolating high purity cpDNA from grasses. The method described
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